EP2576787B1 - Mit polyzystischem ovarialsyndrom assoziierte snps, chips damit und ihre verwendung - Google Patents

Mit polyzystischem ovarialsyndrom assoziierte snps, chips damit und ihre verwendung Download PDF

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Publication number
EP2576787B1
EP2576787B1 EP10852344.0A EP10852344A EP2576787B1 EP 2576787 B1 EP2576787 B1 EP 2576787B1 EP 10852344 A EP10852344 A EP 10852344A EP 2576787 B1 EP2576787 B1 EP 2576787B1
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Prior art keywords
pcos
dna
artificial
thada
snps
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Not-in-force
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EP10852344.0A
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English (en)
French (fr)
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EP2576787A4 (de
EP2576787A1 (de
Inventor
Zijiang Chen
Lin He
Yongyong Shi
Jinlong Ma
Yueran Zhao
Han Zhao
Yuhua Shi
Ling Geng
Li You
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Shanghai Jiaotong University
Shandong University
Shandong Shanda Hospital for Reproductive Medicine Co Ltd
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Shanghai Jiaotong University
Shandong University
Shandong Shanda Hospital for Reproductive Medicine Co Ltd
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes

Definitions

  • This invention relates to SNPs associated with Polycystic Ovary Syndrome, chips comprising the same and the use thereof.
  • Polycystic ovary syndrome is a clinical condition characterized by presence of two or more of these features: chronic oligo-ovulation or anovulation, androgen excess and polycystic ovaries. 1 As the most common cause of anovulatory infertility, PCOS affects 6-8% childbearing-aged women. 2,3 Additionally, PCOS is associated with important endocrine-metabolic derangements and a broad range of adverse sequelae, including dyslipidemia, atherosclerosis, insulin resistance and type 2 diabetes. 4-6 Insulin resistance is present in perhaps 50% of women with PCOS. 7 Among women with impaired glucose tolerance (IGT) and diabetes mellitus, about 20% were recognized at younger age to have PCOS. 8-10
  • PCOS polycystic ovary syndrome
  • An in vitro assay method and assay device for the diagnosis of the presence or the predisposition to suffer from PCOS and/or cardiovascular risk factors including: general obesity, abdominal obesity, hypertension, glucose intolerance, diabetes, hyperinsulinemia, general hypercholesterolemia, hypercholesterolemia with high LDL-cholesterol levels, low HDL-cholesterol levels and hypertriglyceridemia, as well as the grouping of some of these cardiovascular risk factors known as metabolic syndrome.
  • the method and the kit are characterized in that they are based on the detection of at least one genotype or haplotype of a polymorphism in the CAPN5 gene selected from: Nt g.86 A>G Nt g.344 G>A, Nt c.1320 C>T and Nt c. 1469 G>A or combinations thereof.
  • KR20040074800-A - discloses a composition for diagnosis of polycystic ovary syndrome comprising primers detecting single nucleotide polymorphism at 677th nucleotide of 5,10-methylenetetrahydrofolate reductase gene is provided, thereby improving accuracy of diagnosis of polycystic ovary syndrome.
  • the single nucleotide polymorphism at 677th nucleotide of MTHFR gene is selected from cytosine/cytosine(C/C), cytosine/thymine(C/T) and thymine/thymine(T/T).
  • Array based whole genome single-nucleotide polymorphisms (SNPs) association analyses may instead provide a comprehensive, unbiased approach to screen large scale patients to detect susceptibility genes for the diseases.
  • SNPs whole genome single-nucleotide polymorphisms
  • LHCGR encodes a G-protein coupled receptor for luteinizing hormone ( LH ) and choriogonadotropin ( HCG ).
  • LH luteinizing hormone
  • HCG choriogonadotropin
  • LHCGR is expressed in granulosa cells at the later stages of preovulatory follicles.
  • the induction of LHCGR during granulosa cell differentiation allows the preovulatory follicle to respond to the mid-cycle surge of LH, resulting in ovulation and release of the mature oocyte.
  • inactivating (or loss-of-function) mutations of LHCGR are associated with increased LH, enlarged ovaries, oligomenorrhea, resistance to LH or HCG and infertility; 23,24 whereas activating mutations in affected women produce hyperandrogenism but no other effect on reproductive abnormalities. 25
  • THADA peroxisome proliferator-activated receptor gamma
  • THADA The function of THADA has not been well-characterized, but some evidence suggests it might be involved in the death receptor pathway and apoptosis. 32 THADA is extensively expressed in all tissues, and particularly high in lymphocytes, natural killer cells and monocytes. This suggests a role for THADA in the immune response. In the innate and/or adaptive immune response, THADA may participate as a cytokine in the inflammatory signaling pathway causing systemic diseases like PCOS.
  • DENND1A the other associated 9q33.3 gene, encodes a DENN (differentially expressed in normal and neoplastic cells) domain that can hybridize with type-1 tumor necrosis factor receptor (TNFR1 ) as a negative regulator through a death domain-death domain interaction.
  • TNFR1 type-1 tumor necrosis factor receptor
  • DENND1A cannot repress normally, resulting in elevated TNFR1 that further contributes to the induction of apoptosis and activation of the inflammation pathway.
  • THADA and DENND1A seem to play roles in PCOS through a chronic inflammation pathogenesis.
  • CRP C-reactive protein
  • PAI-1 plasminogen activator inhibitor-1
  • the present invention provides THADA, LHCGR and DENND1A genes with SNPs, wherein THADA gene with one or more SNPs of rs11891936 (A/G), rs17030684 (T/C), rs4340576 (G/A), rs12468394 (A/C), rs7567607 (A/G), rs13429458 (C/A), rs7568365(T/C), rs7582497 (G/A), rs10176241 (G/A), rs6744642 (T/C), rs12478601 (T/C), rs1038822(C/T), rs7559891 (A/G), rs1873555 (G/A), rs7596052 (A/G), rs10165527 (A/G), rs6726014 (T/A), rs2374551 (G/C),
  • (M/N) means minor allele/ major allele in the SNP.
  • the present invention further provides an entire set of probes according to claim 1 and its use according to claim 2.
  • the present invention further provides a method according to claim 3 wherein, this method mainly comprises the following steps: extracting the peripheral blood DNA from patients and hybridizing with the entire set of probes of claim 1; scanning and analyzing the results with the associated SNP allele information to predict the risk of PCOS.
  • PCOS cases All affected individuals defined as PCOS cases were diagnosed according to the Revised 2003 Consensus on Diagnostic Criteria and Long-term Health Risks Related to Polycystic Ovary Syndrome 1 , i.e., any two of the following three criteria: oligo- or anovulation, clinical and/or biochemical signs of hyperandrogenism and polycystic ovary morphology. Patients with other causes of oligomenorrhea or hyperandrogenism were excluded. Clinical information was collected from the cases through a full clinical checkup by physician specialists. Additional demographic information was collected from both cases and controls through a structured questionnaire. All participants provided written informed consents. The study was approved by the Institutional Ethical Committee of each hospital and was conducted according to Declaration of Helsinki principles.
  • Genome-wide genotyping was performed using the Affymetrix Genome-Wide Human SNP Array 6.0. Quality control filtering of the GWAS data was performed as follows: the arrays whose Contrast QC was 0.4 or greater being left out of further data analysis. Genotype data were generated using the birdseed algorithm. For sample filtering, array with generated genotypes of fewer than 95% of loci were excluded. For SNP filtering (after sample filtering), SNP with call rates ⁇ 95% in either case or control samples were removed. SNPs whose MAF (minor allele frequency) was ⁇ 1%, or deviated significantly from Hardy Weinberg Equilibrium (HWE, P ⁇ 0.001) in controls were excluded. A total of 649,264 SNPs passed the quality criteria and were used for the subsequence analysis.
  • HWE Hardy Weinberg Equilibrium
  • Allele-specific oligonucleotides to the SNP sequences are printed on epoxy-coated glass microscope slide using a microarray printer. Each set was printed in duplicate so that for each SNP there were four major and minor allele oligonucleotide spots. Twelve such blocks of oligonucleotides were printed on each slide thereby allowing the testing of DNAs from twelve different people per slide.

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  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
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Claims (4)

  1. Vollständiger Satz von Proben mit SNPs, die zur Prognose der Gefahr des polyzystischen Ovarialsyndroms verwendet werden, wobei die Nukleotidsequenzen der Proben durch Seq. ID Nr. 1-56 dargestellt werden.
  2. Verwendung des vollständigen Satzes von Proben nach Anspruch 1 bei der Prognose der Gefahr des polyzystischen Ovarialsyndroms.
  3. Verfahren zur Prognose der Gefahr des polyzystischen Ovarialsyndroms, wobei das Verfahren den vollständigen Satz von Proben nach Anspruch 1 verwendet.
  4. Verfahren nach Anspruch 3, wobei das Verfahren in erster Linie die folgenden Schritte umfasst:
    Extrahieren der peripheren Blut-DNA der Patienten und Hybridisieren mit dem vollständigen Satz von Proben nach Anspruch 1; Scannen und Analysieren der Ergebnisse mit der assoziierten SNP-Allel-Information zur Prognose der Gefahr des polyzystischen Ovarialsyndroms.
EP10852344.0A 2010-05-31 2010-05-31 Mit polyzystischem ovarialsyndrom assoziierte snps, chips damit und ihre verwendung Not-in-force EP2576787B1 (de)

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PCT/CN2010/073387 WO2011150545A1 (en) 2010-05-31 2010-05-31 Snps associated with polycystic ovary syndrome, chips comprising the same and use thereof

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ES2757942T3 (es) * 2012-05-21 2020-04-30 Penn State Res Found Composiciones y métodos relacionados con la variante 2 de dennd1a y síndrome de ovario poliquístico
CN104411824B (zh) * 2012-06-18 2017-12-26 山东大学 与多囊卵巢综合征相关的snp标记
EP4286517A3 (de) 2013-04-04 2024-03-13 President and Fellows of Harvard College Therapeutische verwendungen einer genomänderung mit crispr-/cas-systemen
WO2015077265A1 (en) 2013-11-19 2015-05-28 Virginia Commonwealth University Compositions and methods for prophylaxis and/or therapy of disorders that correlate with dennd1a variant 2
CN104777242B (zh) * 2014-01-14 2016-08-17 中国科学院大连化学物理研究所 用于诊断多囊卵巢综合征的联合标志物、试剂盒和系统
CN104593513A (zh) * 2015-02-06 2015-05-06 上海中优医药高科技有限公司 一种卵巢反应相关基因的基因检测方法
JP6602847B2 (ja) 2015-03-27 2019-11-06 株式会社ボナック デリバリー機能と遺伝子発現制御能を有する一本鎖核酸分子
CN107847524A (zh) 2015-03-27 2018-03-27 哈佛学院校长同事会 经过修饰的t细胞及其制备和使用方法
WO2018195129A1 (en) 2017-04-17 2018-10-25 University Of Maryland, College Park Embryonic cell cultures and methods of using the same
CN109022565B (zh) * 2017-06-12 2022-02-11 山大生殖研发中心有限公司 多囊卵巢综合征的microRNA生物标记物和其应用
CN107190076B (zh) * 2017-06-28 2019-12-27 中国科学院苏州生物医学工程技术研究所 一种人肿瘤相关的甲基化位点及其筛选方法和用途
CN113049838A (zh) * 2019-12-27 2021-06-29 山东大学 多囊卵巢形态阈值和其在诊断多囊卵巢综合征中的应用
CN115364219A (zh) * 2021-12-02 2022-11-22 山东大学 Thada在制备糖代谢紊乱疾病预防及治疗药物中的应用
CN115372626A (zh) * 2022-07-12 2022-11-22 山东大学 Thada在制备糖代谢紊乱疾病筛选试剂中的应用

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WO2011150545A1 (en) 2011-12-08
US20120309642A1 (en) 2012-12-06
CN102918158A (zh) 2013-02-06
EP2576787A4 (de) 2013-04-10
CN102918158B (zh) 2014-05-28
EP2576787A1 (de) 2013-04-10

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